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Showing :
GenomeInfoDb
•
reset
0
votes
3
replies
760
views
Permanent error in installing GenomeInfoDb
GenomeInfoDb
18 months ago
AZ
▴ 30
0
votes
4
replies
1.3k
views
keepStandardChromosomes doesn't respect ordering
genomeinfodb
updated 8.6 years ago by
Sonali Arora
▴ 380 • written 8.6 years ago by
James W. MacDonald
62k
2
votes
2
replies
964
views
How does one modify a single value of a field in a seqinfo object?
GenomicRanges
GenomeInfoDb
BSgenome
isCircular
updated 2.5 years ago by
Hervé Pagès
16k • written 2.7 years ago by
Chris Seidel
▴ 80
1
vote
3
replies
1.2k
views
GenomeInfoDb::Seqinfo() error 404 on the function
GenomeInfoDb
Seqinfo
404 error
6.3 years ago
bastien.herve
• 0
16
votes
10
replies
5.0k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
GenomeInfoDb
updated 3 months ago by
Hervé Pagès
16k • written 19 months ago by
sarah.howles
▴ 20
3
votes
4
replies
2.0k
views
R Error: package ‘GenomeInfoDb’ could not be loaded on MacBook
error
mac
DESeq2
GenomeInfoDb
R
2.4 years ago • updated 2.3 years ago
Dan
▴ 20
1
vote
3
replies
1.4k
views
Unable to GetGRangesFromEnsDb
single
GenomeInfoDb
updated 5 months ago by
Yichao
• 0 • written 16 months ago by
Francesco Monticolo
• 0
7
votes
7
replies
2.8k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi
refseq
maketxdbfromgff
fetchExtendedChromInfoFromUCSC
genomeinfodb
updated 7.4 years ago by
Hervé Pagès
16k • written 7.4 years ago by
gokcen.eraslan
▴ 10
0
votes
1
reply
780
views
GenomeInfoDb: where are the genome patches?
seqnames
genomeinfodb
updated 6.0 years ago by
Hervé Pagès
16k • written 6.0 years ago by
matt.chambers42
▴ 10
0
votes
1
reply
798
views
seqlevels/keepSeqLevels should set default pruning.mode by a getOption call
genomeinfodb
updated 6.0 years ago by
Hervé Pagès
16k • written 6.0 years ago by
matt.chambers42
▴ 10
0
votes
3
replies
5.5k
views
Trouble installing DESeq / GenomeInfoDb
deseq2
genomeinfodb
updated 5.8 years ago by
James W. MacDonald
62k • written 5.8 years ago by
nathan.medd
• 0
1
vote
1
reply
749
views
seqnames versus chrom
BiocGen
rtracklayer
genomeinfodb
updated 5.4 years ago by
Michael Lawrence
11k • written 5.4 years ago by
felix.ernst
• 0
7
votes
5
replies
1.4k
views
Strange error in bsseq when trying to assign seqinfo
bsseq
genomeinfodb
genomicranges
seqinfo
written 5.0 years ago by
rcavalca
▴ 140
0
votes
1
reply
1.4k
views
Issue using ballgown
software error
ballgown
genomeinfodbdata
genomeinfodb
updated 4.7 years ago by
James W. MacDonald
62k • written 4.7 years ago by
dualeahmed
• 0
8
votes
11
replies
2.3k
views
GenomeInfoDb's Seqinfo() error on hg38
genomeinfodb
updated 4.3 years ago by
Hervé Pagès
16k • written 4.3 years ago by
Michael Love
40k
0
votes
7
replies
2.0k
views
Assembly report error for hg19 in GenomeInfoDb
software error
GenomeInfoDb
HTGTS
Transloc-pipeline
TranslocHotspots.R
updated 2.2 years ago by
markus.riester
▴ 130 • written 3.7 years ago by
roshniroy16
• 0
3
votes
5
replies
699
views
Information on genomic sequences via Seqinfo failing
GenomeInfoDb
updated 3.2 years ago by
Hervé Pagès
16k • written 3.2 years ago by
Benilton Carvalho
★ 4.3k
2
votes
3
replies
1.1k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb
hg19
ucsc
seqlevel
genomicfeatures
updated 3.2 years ago by
James W. MacDonald
62k • written 3.2 years ago by
foehn
▴ 80
4
votes
3
replies
920
views
OrganismDbi throws error for Oryza Sativa indica org.db preparation
GenomeInfoDb
OrganismDbi
biomaRt
updated 2.6 years ago by
James W. MacDonald
62k • written 2.6 years ago by
rohitsatyam102
▴ 20
0
votes
2
replies
651
views
Error in GenomeInfoDb:::makeNewSeqnames
GenomeInfoDb
ggbio
2.4 years ago • updated 2.3 years ago
Konstantinos Yeles
▴ 80
1
vote
4
replies
629
views
seqinfo got changed after `library(rtracklayer)`
rtracklayer
GenomeInfoDb
17 months ago
Ge Tan
▴ 20
1
vote
2
replies
748
views
Error in csaw::windowCounts when using readParam
csaw
GenomeInfoDb
updated 2.7 years ago by
Aaron Lun
★ 28k • written 2.7 years ago by
RichardJActon
▴ 50
0
votes
2
replies
1.5k
views
GenomeinfoDB
Mus musculus
GenomeInfoDb
Mus musculus
GenomeInfoDb
updated 8.9 years ago by
Sonali Arora
▴ 380 • written 8.9 years ago by
Guest User
★ 12k
6
votes
2
replies
4.7k
views
Get sequences for GRCh38 genome based on TxDb object locations
bsgenome
genomeinfodb
transcriptdb
updated 8.4 years ago by
Hervé Pagès
16k • written 8.4 years ago by
Diego Diez
▴ 760
2
votes
5
replies
1.3k
views
GenomeInfoDb::extractSeqlevelsByGroup() on 'Canis familiaris'
genomeinfodb
canis familiaris
updated 7.6 years ago by
Hervé Pagès
16k • written 7.6 years ago by
Robert Castelo
★ 3.0k
4
votes
9
replies
3.5k
views
Is it possible to read bigwig files with rtracklayer over https? Comes down to GenomeInfoDb::seqinfo()
rtracklayer
genomeinfodb
7.1 years ago
Leonardo Collado Torres
★ 1.0k
3
votes
3
replies
2.4k
views
keepSeqlevels for GRangesList: drop elements with multiple seqnames
GenomeInfoDb
keepSeqlevels
updated 6.5 years ago by
Valerie Obenchain
★ 6.7k • written 6.6 years ago by
Chao-Jen Wong
▴ 30
0
votes
7
replies
1.5k
views
regionMatrix for derfinder crashes with seqnames issue on non-human data
derfinder
GenomeInfoDb
GenomicRanges
6.1 years ago
Wayne
• 0
0
votes
2
replies
855
views
seqlevelsStyle for chrY in Drosophila?
genomeinfodb
dmel
seqlevelsstyle
updated 6.0 years ago by
daniel.vantwisk
▴ 50 • written 6.0 years ago by
liz.ingsimmons
▴ 140
3
votes
2
replies
708
views
Please allow integers in `numeric` format in `seqlengths`
GenomeInfoDb
updated 18 months ago by
Hervé Pagès
16k • written 18 months ago by
Charles Plessy
▴ 170
0
votes
1
reply
122
views
package ‘GenomeInfoDb’ could not be loaded
GenomeInfoDb
GenomeInfoDbData
updated 12 weeks ago by
ATpoint
★ 2.8k • written 12 weeks ago by
exferin
• 0
0
votes
2
replies
1.4k
views
GenomeInfoDb fails to install
zip
GenomeInfoDb
updated 21 months ago by
Marcel Ramos
660 • written 21 months ago by
David
• 0
3
votes
2
replies
3.1k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m31) is not TRUE
GenomeInfoDb
updated 22 months ago by
Rob Syme
▴ 20 • written 23 months ago by
jason.ossart
▴ 10
1
vote
5
replies
658
views
Unable to load mm10 genome for use with GenomicDistributions package
GenomeInfoDb
GenomeInfoDbData
GenomicDistributionsData
GenomicDistributions
11 months ago
rashford
• 0
0
votes
0
replies
1.0k
views
'GenomeInfoDb' error in the cn.MOPS Package
cnv
genomeinfodb
7.9 years ago
voksdvoks
• 0
0
votes
1
reply
407
views
RNA gene expression data retrieval for breast cancer subtypes
RNASeqData
GenomeInfoDb
updated 2.5 years ago by
Kevin Blighe
3.8k • written 2.5 years ago by
G.G.H.T.
• 0
0
votes
0
replies
555
views
motifBreakR error with custom BSgenome
GenomeInfoDb
motifbreakR
2.1 years ago
Chris Seidel
▴ 80
0
votes
1
reply
1.1k
views
errotr in genome infodb
software error
roar
bioconductor
genomeinfodb
5.9 years ago
praveenhcu131
• 0
0
votes
1
reply
629
views
GenomeInfoDbData cannot install in R and warning had non-zero exit status
GenomeInfoDb
updated 14 months ago by
James W. MacDonald
62k • written 14 months ago by
yt_lei1998
• 0
39 results • Page
1 of 1
Recent ...
Replies
Comment: Visualization of negative log CPM values
by
Gordon Smyth
47k
Sorry, but some of the things you say are not correct. > compound B has 2 statistically significant genes that are up-regulated No, there…
Comment: Visualization of negative log CPM values
by
ATpoint
★ 2.8k
Applies to both.
Comment: Visualization of negative log CPM values
by
Sabiha
▴ 10
@atpoint OK, are you referring to the `log2(cpm+1)` or `log2(tpm+1)`
Comment: Visualization of negative log CPM values
by
Sabiha
▴ 10
@gordonsmyth noted. Related to the graphs above, the table below is the output from `limma`, and compound B has 2 statistically significant…
Comment: Visualization of negative log CPM values
by
Gordon Smyth
47k
> negative scale might perhaps indicate gene is too low to be really expressed. Yes, negative logCPMs do mean that the gene is expressed a…
Votes
Comment: Visualization of negative log CPM values
Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?
Filtering low intensity probes in microarray data
Comment: Visualization of negative log CPM values
Adjusting for baseline when having longitudinal data, mixed model and no treatment
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